Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection

ABSTRACT: Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection

PROVIDER: PRJNA344999 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR4310480.fastq.gz	Fastqsanger.gz
	SRR4310481.fastq.gz	Fastqsanger.gz
	SRR4310472.fastq.gz	Fastqsanger.gz
	SRR4310482.fastq.gz	Fastqsanger.gz
	SRR4310473.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Host and genetic viral adaptations enable development of an immunocompetent mouse model of Zika virus infection

Project description:Host and genetic viral adaptations enable development of an immunocompetent mouse model of Zika virus infection. This study explored the effect of wildtype Zika virus (ZIKV) and mouse adapted ZIKV infection on the transcriptional profile of mouse adult neuronal stem cells.

2018-04-05 | GSE112711 | GEO

Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

Project description:Zika virus (ZIKV) and dengue virus (DENV) are members of the Flaviviridae family of RNA viruses and cause severe disease in humans. ZIKV and DENV share over 90% of their genome sequences, however the clinical features of Zika and dengue infections are very different reflecting tropism and cellular effects. Here, we used simultaneous RNA sequencing and ribosome footprinting to define the transcriptional and translational dynamics of ZIKV and DENV infection in human neuronal progenitor cells (hNPCs). The gene expression data showed induction of aminoacyl tRNA synthetases (ARS) and the translation-activating PIM1 kinase indicating an increase in RNA translation capacity. The data also reveal activation of different cell stress reponses, with ZIKV triggering a BACH1/2 redox program, and DENV activating the ETF/CHOP endoplasmatic reticulum (ER) stress program. The RNA translation data highlight activation of polyamine metabolism through changes in key enzymes and their regulators. This pathway is needed for eIF5A hypusination and has been implicated viral translation and replication. Concerning the viral RNA genomes, ribosome occupancy readily identifies highly translated open reading frames and a novel upstream ORF (uORF) in the DENV genome. Together, our data highlight both the cellular stress response and also the activation of RNA translation and polyamine metabolism during DENV and ZIKV infection.

2022-07-06 | GSE207347 | GEO

Dynamics of Human and Viral RNA Methylation during ZIKA Virus Infection

Project description:Human infection with the flavivirus ZIKA (ZIKV) causes severe neurological, immunological, and developmental defects. Despite recent progress, the mechanisms by which ZIKV infection alters host transcriptional and translational programs remains unclear. Here, we report that ZIKV infection has profound effects on the topology and function of N6-adenosine methylation (m6A) of both viral and human RNAs. m6A and 2′-O-methylated nucleosides are abundant in ZIKV genomic RNA, and m6A-seq identified 12 m6A peaks spanning the full length of ZIKV RNA. m6A abundance in ZIKV RNA is controlled by the host methyltransferases METTL3 and METTL14 and the demethylase ALKBH5. Profiling of the m6A methylome of host mRNAs revealed that ZIKV infection alters the location of m6A in mRNAs, the methylation motifs, and the target genes modified by the methyltransferases. Our results identify a new mechanism by which ZIKV interacts with and alters the function of the host cell.

2016-11-15 | GSE87516 | GEO

CRISPR screen for the identification of host factors for ZIKA virus infection

Project description:To search for host factors regulating Zika virus infection, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of enrichment of their mutant clones within a pooled loss-of-function library upon Zika virus infection.

2023-05-31 | E-MTAB-11945 | biostudies-arrayexpress

Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

Project description:Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

| PRJNA854905 | ENA

Single cell transcriptional dynamics of flavivirus infection

Project description:Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.

2018-02-27 | GSE110496 | GEO

MiSeq analysis of viral progeny at 24 and 72 hours post-infection with H/PF/2013 Zika virus of HuH-7 cells

Project description:To better understand mutations that can contribute to Zika pathogenesis, we allow the H/PF/2013 wild-type strain to replicate in HuH-7 cells to analyze the population of viral variants.

2021-05-24 | E-MTAB-10474 | biostudies-arrayexpress

Zika virus

Project description:Zika Virus Virus genome sequencing

| PRJNA336379 | ENA

Inter and intra-lineage genetic diversity of Zika virus differs for American isolates

Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.

2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress

SVG cells infected with Zika virus for 24, 48 and 72 hr post infection

Project description:Transcriptional profiling of human astrocyte cells (SVG) infected with Zika virus. Goal was to identify temporal changes in gene expression post infected by Zika virus.

2017-10-13 | GSE89915 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data